Abstract
Coronaviruses (CoVs) belonging to the Gamma-CoV and Delta-CoV genera are widespread in poultry and wildfowl. Migratory birds, particularly duck species, serve as hosts for CoVs and play a pivotal role in transmitting the viruses to other species, including mammals. Despite the potential risks to animals and humans, there remains a narrow knowledge of the genetic and epidemiological properties of CoVs in wild birds. The current research aimed to detect and characterize CoVs present in migratory duck species (Anas acuta, Anas platyrhynchos, and Anas poecilorhyncha) from South Korea. Employing two rounds of pan-CoV real-time reverse transcription-polymerase chain reaction (RT-PCR) and nested PCR (nPCR) assays amplifying the conserved RNA-dependent RNA polymerase (RdRp) portion common to all known CoVs, we screened 2120 duck fecal samples collected during 2022-2023. The results indicated the presence of CoVs in 4.2% (91/2120) of samples from migratory ducks. Nucleotide sequencing of the RdRp gene revealed that all identified CoVs were clustered within the Gamma-CoV genus. Further phylogenetic analysis suggested that South Korean gamma-CoVs belong to the Igacovirus subgenus and share similarities with those found worldwide, highlighting the critical role of migratory ducks in introducing and exporting avian CoVs. We discovered two clade VII igacovirus strains in wild ducks closely related to those in pigeons, implying potential cross infection between these avian species. Overall, our study underscores the importance of active surveillance and monitoring of avian CoVs in wild birds as a preemptive response against the forthcoming emergence of new CoV species that can threaten both animal and human health.